This is a bit late, but some of the opinions I'm seeing here make me pretty sad. I always knew that the internet was oversensitive to Mary-Sue accusations, but we're stretching the definition, here.
The biggest defining point of the Mary-Sue is thus: Does the universe bend for them? If it doesn't, and if the character makes mistakes, then what we're dealing with is not a Mary-Sue.
I've met people like Kvothe, they're real. He's a prodigy, and is exceptional at most of the things he tries. This isn't a magical impossible thing, it happens in real life. What we're also ignoring, when we call Kvothe a sue, is how many times he almost gets himself killed. Half of the "heroic" things he does are stupid at best, retarded at worst. Most of the "dangerous" situations throughout the series are ones that he gets himself into.
Also, Kvothe's infatuation with Denna is simple: She was the first girl he ever connected with. He was a poor kid with no friends, and he talked to her and got along with her. If you aren't aware immediately by reading: young Kvothe (and occasionally old Kvothe) wears his emotions on his sleeve. It's part of the reason why he's so impulsive. He fell in love with her when he was a kid, and he can't let it go. His obsession with her is idealized to the point that he may not even see who she really is anymore. (Years later, Bast still has to remind him that she had a hook-nose.)
Personally, I think that there are a LOT of interesting female characters, but they show up later on. Unfortunately, the story follows Kvothe, and he spent most of his early life away from women. Devi, in particular, fascinates me.
Personally, this is one of my favorite books, but to each his own.